Mercurial > repos > iuc > mothur_anosim

annotate anosim.xml @ 0:08ccc12f2a3a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:39:40 -0400
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children d83e7e498f31
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_anosim" name="Anosim" version="@WRAPPER_VERSION@.0">
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Non-parametric multivariate analysis of changes in community structure</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$dist" dist.dat &&
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$design" design.dat &&
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15
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16 echo 'anosim(
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 phylip=dist.dat,
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18 iters=$iters,
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19 alpha=$alpha,
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 design=design.dat
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21 )'
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22 | sed 's/ //g' ## mothur trips over whitespace
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23 | mothur
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24 | tee mothur.out.log
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25 ]]></command>
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26 <inputs>
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27 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 <param name="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision (default 0.05)"/>
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 </inputs>
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32 <outputs>
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33 <expand macro="logfile-output"/>
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34 <data name="anosim" format="tabular" from_work_dir="dist.anosim" label="${tool.name} on ${on_string}: anosim"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="dist" value="amazon.dist"/>
08ccc12f2a3a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <param name="design" value="amazon.design"/>
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40 <output name="anosim" ftype="tabular">
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41 <assert_contents>
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42 <has_line_matching expression="^comparison\tR-value\tP-value$"/>
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43 <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/>
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44 </assert_contents>
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45 </output>
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46 <expand macro="logfile-test"/>
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
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51
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52 @MOTHUR_OVERVIEW@
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53
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54 **Command Documentation**
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55
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56 The anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure.
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57
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58 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
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59 ======= =======
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60 duck bird
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61 cow mammal
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62 pig mammal
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63 goose bird
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64 cobra reptile
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65 ======= =======
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66
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67 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
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68
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69
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70 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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71 .. _anosim: https://www.mothur.org/wiki/Anosim
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72
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73 ]]>
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74 </help>
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75 <expand macro="citations"/>
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76 </tool>